Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study)/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27
Curated date: 2021/09/27
Curator: Gina
Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Gina, Peace Sandy
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 7 week old (young) mice before antibiotic treatment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 7 week old (young) mice 10 days after antibiotic treatments
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 7-week old mice (young mice) administered treated with broad-spectrum antibiotics metronidazole (500 mg/L) and ciprofloxacin (200 mg/L) for 10 days.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Mice were not previously given antibiotics before the study
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27
Source: Figure 5
Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young mice after 10 days of antibiotic treatment
Abundance in Group 1: increased abundance in 7 week old (young) mice 10 days after antibiotic treatments
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcaceae | ||
| Lactobacillales | ||
| Enterococcus |
Revision editor(s): Gina
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/27
Source: Figure 5
Description: Linear discriminant analysis (LDA) effect size (LEfSe) of differentially abundant bacterial taxa between young after 10 days of Abx treatment
Abundance in Group 1: decreased abundance in 7 week old (young) mice 10 days after antibiotic treatments
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Stoquefichus | ||
| Clostridiales Family XIII bacterium | ||
| Erysipelotrichaceae | ||
| Erysipelotrichales | ||
| Faecalibaculum | ||
| Peptostreptococcaceae | ||
| Romboutsia | ||
| Clostridiales bacterium |
Revision editor(s): Gina
